SLE

EDA

Overall

Demographic and Clinical Characteristics
Variable Category Value
Age at Diagnosis - 29.0 ± 13.3 (0-80)
Sex Male 210 (11.6%)
Female 1593 (88.2%)
Race White 1024 (56.7%)
Black 274 (15.2%)
Chinese 195 (10.8%)
Other 123 (6.8%)
Native North American 16 (0.9%)
Filipino 76 (4.2%)
Mixed 34 (1.9%)
Vital Status Active 1191 (65.9%)
Dead 209 (11.6%)
Lost to Follow-up 5 (0.3%)
Green Chart 378 (20.9%)
Discharged from Clinic 1 (0.1%)
No Consent 3 (0.2%)
Questionnaire 18 (1.0%)
Employment Status disabled 317 (17.6%)
sick leave 66 (3.7%)
homemaker 165 (9.1%)
retired 163 (9.0%)
student 215 (11.9%)
looking for work 45 (2.5%)
employed 835 (46.2%)
Number of Visits - 28.5 ± 27.6 (1-179)

By Employment Status

Employment Status Characteristics with Transition History
Counts
Sex
Age (Diagnosis)
Age (1st Vist)
Race
Status
Employment Status N % of Cohort % Male % Female Mean Age (At Diagnosis) SD Age Median Age Mean Age (1st Visit) SD Age (1st Visit) Median Age (1st Visit) % White % Black % Chinese % Other % Native % Filipino % Mixed % Active % Dead % Lost % Green Chart % Discharged % No Consent % Questionnaire % Questionnaire2
Employed 803 44.5% 12.1% 87.9% 30.1 11.4 29 38.1 11.2 36.9 61.5% 15.3% 9.5% 6.6% 0.5% 4.7% 1.8% 73.3% 7.9% 0.5% 17.2% 0.0% 0.1% 1.0% 0.0%
Future Workforce 420 23.3% 13.4% 86.6% 17.6 6.7 16 22.4 6.4 19.7 45.3% 16.6% 20.0% 9.9% 0.7% 4.5% 3.0% 70.7% 5.7% 0.2% 22.9% 0.2% 0.0% 0.2% 0.0%
Permanent exit 295 16.3% 14.2% 85.8% 37.5 14.9 35 49.4 14.0 49.6 65.0% 17.6% 7.3% 3.8% 2.1% 3.5% 0.7% 45.1% 26.4% 0.0% 26.1% 0.0% 0.0% 2.4% 0.0%
Temporary exit 288 16.0% 5.2% 94.8% 33.5 12.9 31 42.7 13.3 41.1 64.3% 13.6% 7.1% 7.5% 1.1% 4.3% 2.1% 60.1% 15.3% 0.0% 23.3% 0.0% 0.7% 0.7% 0.0%
Employment Transition Summary by Initial Employment Status
Employment Status N Median Visits Visit Range IQR Visits Median Obs (months) Median Transitions Transition Range Initial SLEDAI Final SLEDAI Mean SLEDAI Ever Retired Ever Disabled Ever Homemaker Ever Student Ever Looking Ever Employed Ever Sick Leave Final Retired Final Disabled Final Homemaker Final Student Final Looking Final Employed Final Sick Leave Changed Status
Employed 803 17 1 - 94 7 - 35 108.19645 0 0 - 8 4 2 3.200000 61 (7.6%) 103 (12.8%) 33 (4.1%) 23 (2.9%) 38 (4.7%) 803 (100%) 63 (7.8%) 58 (7.2%) 78 (9.7%) 19 (2.4%) 7 (0.9%) 11 (1.4%) 609 (75.8%) 21 (2.6%) 249 (31%)
Future Workforce 420 13 1 - 85 7 - 25 93.44612 0 0 - 8 4 3 4.000000 1 (0.2%) 29 (6.9%) 7 (1.7%) 373 (88.8%) 75 (17.9%) 183 (43.6%) 19 (4.5%) 0 (0%) 18 (4.3%) 3 (0.7%) 206 (49%) 29 (6.9%) 156 (37.1%) 8 (1.9%) 204 (48.6%)
Permanent exit 295 17 1 - 91 6 - 33 101.14980 0 0 - 4 4 2 3.387755 90 (30.5%) 218 (73.9%) 8 (2.7%) 2 (0.7%) 4 (1.4%) 23 (7.8%) 4 (1.4%) 86 (29.2%) 182 (61.7%) 5 (1.7%) 0 (0%) 1 (0.3%) 18 (6.1%) 3 (1%) 36 (12.2%)
Temporary exit 288 20 1 - 93 8 - 39 118.90604 0 0 - 9 5 2 3.022080 19 (6.6%) 52 (18.1%) 203 (70.5%) 14 (4.9%) 14 (4.9%) 66 (22.9%) 102 (35.4%) 19 (6.6%) 39 (13.5%) 138 (47.9%) 2 (0.7%) 4 (1.4%) 52 (18.1%) 34 (11.8%) 124 (43.1%)
Note:
Values show count (percentage) unless otherwise specified. SLEDAI scores are medians.
Proportion of Patients by Initial Employment State with Exactly N Transitions
Number of Transitions
Initial Employment State 0 1 2 3 4 5 6 7 8 9
Employed 69.0% 17.8% 7.1% 3.2% 1.5% 0.6% 0.4% 0.2% 0.1% 0.0%
Future Workforce 51.4% 35.2% 6.4% 3.3% 1.7% 0.7% 0.5% 0.2% 0.5% 0.0%
Temporary exit 56.9% 29.2% 5.6% 4.5% 2.1% 0.7% 0.0% 0.3% 0.0% 0.7%
Permanent exit 87.8% 7.1% 3.4% 1.0% 0.7% 0.0% 0.0% 0.0% 0.0% 0.0%

Most Common Transitions From Each Status
Origin Age Group Most Common Next State Proportion Total Transitions
Employed 20-29 Future Workforce 58.0% 81
Employed 30-39 Temporary exit 46.7% 92
Employed 40-49 Temporary exit 47.5% 80
Employed 50-59 Permanent exit 65.9% 82
Employed 60-69 Permanent exit 78.4% 37
Employed 70+ Permanent exit 100.0% 9
Employed <20 Future Workforce 90.9% 11
Future Workforce 20-29 Employed 84.4% 186
Future Workforce 30-39 Employed 73.1% 52
Future Workforce 40-49 Employed 71.9% 32
Future Workforce 50-59 Employed 72.7% 11
Future Workforce 60-69 Employed 66.7% 3
Future Workforce <20 Employed 96.0% 25
Permanent exit 20-29 Employed 56.2% 16
Permanent exit 30-39 Employed 75.9% 29
Permanent exit 40-49 Employed 61.9% 21
Permanent exit 50-59 Employed 54.2% 24
Permanent exit 60-69 Temporary exit 60.0% 10
Permanent exit 70+ Temporary exit 100.0% 2
Permanent exit <20 Future Workforce 100.0% 1
Temporary exit 20-29 Employed 38.2% 34
Temporary exit 30-39 Employed 64.9% 77
Temporary exit 40-49 Employed 54.1% 61
Temporary exit 50-59 Permanent exit 71.1% 38
Temporary exit 60-69 Permanent exit 72.2% 18
Temporary exit 70+ Permanent exit 100.0% 7
Temporary exit <20 Future Workforce 100.0% 3

Disease Activity

Slicc Damage Index

Final Status

Dates

Analysis

Markov Transition Matrix

## [1] "First Transition Counts:"
##                   to_state
## from_state         Employed Future Workforce Permanent exit Temporary exit
##   Employed              749                9             10             12
##   Future Workforce       20              388              4              2
##   Permanent exit          0                1            275              1
##   Temporary exit         10                5              6            259
## [1] "\nFirst Transition Probability Matrix:"
##                   to_state
## from_state         Employed Future Workforce Permanent exit Temporary exit
##   Employed            0.960            0.012          0.013          0.015
##   Future Workforce    0.048            0.937          0.010          0.005
##   Permanent exit      0.000            0.004          0.993          0.004
##   Temporary exit      0.036            0.018          0.021          0.925

## [1] "Transition Counts:"
##                   to_state
## from_state         Employed Future Workforce Permanent exit Temporary exit
##   Employed            16995              108            155            129
##   Future Workforce      252             4406             34             23
##   Permanent exit         61               13          10312             29
##   Temporary exit        111               28             99           6091
## [1] "\nTransition Probability Matrix:"
##                   to_state
## from_state         Employed Future Workforce Permanent exit Temporary exit
##   Employed            0.977            0.006          0.009          0.007
##   Future Workforce    0.053            0.934          0.007          0.005
##   Permanent exit      0.006            0.001          0.990          0.003
##   Temporary exit      0.018            0.004          0.016          0.962

Competing Risk Analysis

`

## Call:
## coxph(formula = Surv(time, event) ~ state + AGE_DX + SEX + SLEDAI2_I, 
##     data = surv_data)
## 
##   n= 1800, number of events= 209 
##    (6 observations deleted due to missingness)
## 
##                            coef exp(coef)  se(coef)      z Pr(>|z|)    
## stateFuture Workforce  0.345053  1.412065  0.253552  1.361  0.17355    
## statePermanent exit    1.083942  2.956311  0.178436  6.075 1.24e-09 ***
## stateTemporary exit    0.566421  1.761950  0.198284  2.857  0.00428 ** 
## AGE_DX                 0.030682  1.031158  0.005346  5.739 9.51e-09 ***
## SEXFemale             -0.426687  0.652668  0.190219 -2.243  0.02489 *  
## SLEDAI2_I             -0.004703  0.995308  0.010698 -0.440  0.66020    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
##                       exp(coef) exp(-coef) lower .95 upper .95
## stateFuture Workforce    1.4121     0.7082    0.8591    2.3210
## statePermanent exit      2.9563     0.3383    2.0838    4.1941
## stateTemporary exit      1.7619     0.5676    1.1946    2.5988
## AGE_DX                   1.0312     0.9698    1.0204    1.0420
## SEXFemale                0.6527     1.5322    0.4495    0.9476
## SLEDAI2_I                0.9953     1.0047    0.9747    1.0164
## 
## Concordance= 0.707  (se = 0.02 )
## Likelihood ratio test= 109.3  on 6 df,   p=<2e-16
## Wald test            = 125.9  on 6 df,   p=<2e-16
## Score (logrank) test = 137.7  on 6 df,   p=<2e-16

Markov model

##                   to_state
## from_state         Employed Future Workforce Permanent exit Temporary exit
##   Employed            16995              108            155            129
##   Future Workforce      252             4406             34             23
##   Permanent exit         61               13          10312             29
##   Temporary exit        111               28             99           6091

Trajectories

## # A tibble: 10 × 3
##    simplified_trajectory                          n   prop
##    <chr>                                      <int>  <dbl>
##  1 Future Workforce → Employed                  144 0.235 
##  2 Employed → Permanent exit                    101 0.165 
##  3 Temporary exit → Permanent exit               47 0.0767
##  4 Employed → Temporary exit                     37 0.0604
##  5 Temporary exit → Employed                     37 0.0604
##  6 Employed → Future Workforce                   17 0.0277
##  7 Employed → Temporary exit → Permanent exit    16 0.0261
##  8 Employed → Future Workforce → Employed        15 0.0245
##  9 Permanent exit → Employed                     15 0.0245
## 10 Employed → Temporary exit → Employed          13 0.0212

## 
## Data validation:
## Unique initial states: Permanent exit, Temporary exit, Employed, Future Workforce
## Time range (years): 0 28.13415
## Number of transitions to 'disabled': 529
## quartz_off_screen 
##                 2
Kaplan Meier Plot
Kaplan Meier Plot
## 
## Data validation:
## Unique initial states: Permanent exit, Temporary exit, Employed, Future Workforce
## Time range (years): 0 28.13415
## Number of transitions to 'disabled': 160
## quartz_off_screen 
##                 2
Retired Kaplan Meier Plot
Retired Kaplan Meier Plot